Contacts of the helix formed by residues 689 - 726 (chain A) in PDB entry 1N54
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 689 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A ALA 4.3 2.3 - - - +
663A LYS 4.4 0.5 - - - +
665A LYS* 2.5 37.5 - - + +
688A LEU* 1.3 81.8 - - + +
690A GLU* 1.3 50.5 + - - +
691A GLN* 2.5 23.0 + - - +
692A ILE* 2.6 47.1 + - + +
693A GLU 3.9 0.7 + - - -
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Residues in contact with GLU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A LEU* 3.0 15.8 + - - +
689A GLU* 1.3 74.5 - - - +
691A GLN* 1.3 57.7 + - - +
692A ILE 3.4 0.4 - - - -
693A GLU* 3.5 21.1 - - + +
694A ARG* 3.1 26.5 + - - +
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Residues in contact with GLN 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A GLU* 5.0 2.4 + - - -
662A ALA* 5.1 6.3 - - + -
688A LEU 3.8 7.6 + - - +
689A GLU* 2.5 11.3 + - - +
690A GLU* 1.3 75.5 - - - +
692A ILE* 1.3 55.8 + - + +
694A ARG* 2.9 42.7 + - - +
695A LEU* 2.7 68.1 + - + +
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Residues in contact with ILE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 3.6 19.5 - - + +
662A ALA* 3.8 17.7 - - + -
663A LYS* 3.9 42.4 - - + +
689A GLU* 2.6 52.0 + - + +
691A GLN* 1.3 73.4 - - + +
693A GLU* 1.3 52.9 + - - +
695A LEU* 4.4 2.5 - - - -
696A GLN* 2.7 40.2 + - + +
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Residues in contact with GLU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A GLU 3.9 1.0 + - - -
690A GLU* 3.5 24.1 + - - +
691A GLN 3.2 0.2 - - - -
692A ILE* 1.3 77.1 - - - +
694A ARG* 1.3 66.2 + - - +
696A GLN* 3.8 5.0 - - - +
697A GLU* 3.1 34.8 + - - +
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Residues in contact with ARG 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A GLU* 5.8 0.2 + - - -
690A GLU* 3.1 12.8 + - - +
691A GLN* 2.9 46.9 + - - +
693A GLU* 1.3 83.7 + - - +
695A LEU* 1.3 67.1 + - + +
697A GLU* 3.6 7.8 + - - +
698A LYS* 3.1 35.8 + - + +
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Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A ILE* 4.2 17.9 - - + -
658A GLU* 3.5 53.8 - - + +
659A LEU* 3.4 20.2 - - + +
662A ALA* 4.3 6.5 - - + -
691A GLN* 2.7 49.6 + - + +
694A ARG* 1.3 77.2 - - - +
696A GLN* 1.3 55.2 + - - +
698A LYS* 2.6 34.3 + - + +
699A VAL* 2.7 21.1 + - - +
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Residues in contact with GLN 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 3.3 27.0 - - + +
663A LYS* 3.7 12.3 - - - +
692A ILE* 2.7 26.2 + - + +
693A GLU* 3.8 5.8 - - - +
695A LEU* 1.3 72.6 - - - +
697A GLU* 1.3 60.6 + - - +
699A VAL* 3.4 7.4 + - - +
700A GLU* 2.3 59.4 + - + +
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Residues in contact with GLU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A GLU* 3.1 24.6 + - + +
694A ARG* 3.7 8.2 - - - +
696A GLN* 1.3 80.3 - - - +
698A LYS* 1.3 60.5 + - - +
700A GLU* 3.4 11.7 - - + +
701A SER* 3.4 24.7 + - - +
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Residues in contact with LYS 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A HIS* 4.5 9.9 + - - -
655A ILE* 3.8 30.5 - - + +
658A GLU* 5.9 0.8 + - - -
694A ARG* 3.1 30.6 + - + +
695A LEU* 2.6 30.6 + - + +
697A GLU* 1.3 70.1 - - - +
699A VAL* 1.3 52.7 + - - +
701A SER* 3.2 7.8 + - - +
702A ALA* 2.7 36.4 + - - +
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Residues in contact with VAL 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A VAL* 5.6 1.6 - - + +
655A ILE* 3.5 31.6 - - + +
656A GLN* 4.8 15.9 - - + -
659A LEU* 3.9 23.6 - - + -
695A LEU 2.7 23.7 + - - +
696A GLN* 3.6 7.9 - - - +
698A LYS* 1.3 71.8 - - - +
700A GLU* 1.3 68.2 + - - +
702A ALA* 2.8 6.3 + - + +
703A GLN* 2.8 53.6 + - + +
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A GLN* 2.3 43.4 - - + +
697A GLU* 3.4 14.1 - - + +
699A VAL* 1.3 79.3 - - - +
701A SER* 1.3 59.0 + - - +
703A GLN* 3.4 11.9 + - - +
704A SER* 3.0 29.3 + - - -
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Residues in contact with SER 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A GLU* 3.4 13.8 + - - +
698A LYS* 3.2 11.5 + - - -
699A VAL 3.2 0.4 - - - -
700A GLU* 1.3 75.5 - - - +
702A ALA* 1.3 65.6 + - - +
704A SER* 3.8 7.2 - - - -
705A GLU* 3.3 24.4 + - - +
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Residues in contact with ALA 702 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A MET* 3.4 23.2 - - - +
651A HIS* 4.1 18.6 - - + +
652A VAL* 3.7 14.8 - - + +
655A ILE* 3.8 23.6 - - + -
698A LYS 2.7 21.9 + - - +
699A VAL* 2.8 7.8 + - + +
701A SER* 1.3 73.7 - - - +
703A GLN* 1.3 61.8 + - + +
705A GLU* 4.3 2.0 - - - +
706A GLN* 3.5 7.8 + - - +
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Residues in contact with GLN 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A VAL* 3.9 22.9 - - + +
656A GLN* 5.0 8.2 + - - -
699A VAL* 2.8 41.4 + - + +
700A GLU* 4.0 12.2 + - - +
702A ALA* 1.3 76.4 - - - +
704A SER* 1.3 57.9 + - - +
705A GLU 3.1 1.6 - - - -
706A GLN* 2.5 39.5 + - - +
707A LYS* 2.7 14.8 + - - +
760A GLN* 4.3 16.5 + - - -
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Residues in contact with SER 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A GLU 3.0 19.5 + - - -
701A SER* 3.8 9.9 - - - -
703A GLN* 1.3 76.2 - - - +
705A GLU* 1.3 56.8 + - - +
707A LYS* 3.3 8.5 + - - +
708A ASN* 3.0 27.4 + - - +
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Residues in contact with GLU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A ASP* 3.9 17.5 - - - +
616A CYS* 3.3 31.7 + - + +
617A ALA* 5.0 6.0 + - + +
648A MET* 3.7 19.0 - - - +
651A HIS* 4.9 7.3 + - - -
701A SER 3.3 15.3 + - - +
702A ALA* 4.3 1.5 - - - +
703A GLN 3.1 0.6 - - - -
704A SER* 1.3 75.3 - - - +
706A GLN* 1.3 61.2 + - - +
708A ASN* 3.5 9.9 + - + +
709A LEU* 3.0 27.9 + - - +
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Residues in contact with GLN 706 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A MET* 3.9 22.4 - - + -
649A ASN* 3.4 18.2 + - - -
652A VAL* 3.2 32.4 - - + +
702A ALA 3.5 12.3 + - - +
703A GLN* 2.5 33.9 + - - +
705A GLU* 1.3 72.8 - - - +
707A LYS* 1.3 62.2 + - - +
709A LEU* 3.3 8.4 - - - +
710A PHE* 3.2 33.4 - - + -
757A ILE* 3.7 20.0 - - - +
760A GLN* 4.8 6.5 + - - +
761A TYR* 3.3 20.0 + - - +
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Residues in contact with LYS 707 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A GLN 2.7 14.2 + - - +
704A SER* 3.5 11.9 - - - +
706A GLN* 1.3 70.3 - - - +
708A ASN* 1.3 67.9 + - - +
709A LEU 3.0 0.7 + - - -
710A PHE* 3.1 5.4 + - - +
711A LEU* 2.8 33.7 + - + +
760A GLN 5.2 3.6 + - - -
761A TYR* 3.4 47.9 + - + +
763A VAL* 6.2 2.2 - - - +
764A THR* 3.8 25.7 + - - -
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Residues in contact with ASN 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A ALA* 4.2 19.8 - - - +
704A SER 3.0 14.4 + - - +
705A GLU* 3.6 11.0 + - - +
707A LYS* 1.3 79.3 - - - +
709A LEU* 1.3 51.3 + - - +
711A LEU* 3.1 14.2 + - - +
712A VAL* 2.7 54.4 + - - +
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Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A CYS* 4.4 24.5 - - + +
617A ALA* 5.0 4.5 - - - +
620A ALA* 4.3 16.8 - - + -
641A LEU* 5.3 2.9 - - + -
644A THR* 4.7 3.4 - - + +
645A ILE* 4.0 32.3 - - + -
648A MET* 4.2 23.1 - - + -
705A GLU 3.0 14.4 + - - +
706A GLN* 3.3 12.3 - - - +
707A LYS 3.0 0.4 + - - -
708A ASN* 1.3 76.1 - - - +
710A PHE* 1.3 64.9 + - + +
712A VAL* 3.0 7.1 + - - +
713A ILE* 2.8 51.6 + - + +
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Residues in contact with PHE 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ILE* 3.9 23.1 - - + -
648A MET* 5.8 0.2 - - + -
649A ASN* 4.2 10.5 - - - -
706A GLN* 3.2 32.1 - - + -
707A LYS 3.1 4.9 + - - +
709A LEU* 1.3 81.4 - - + +
711A LEU* 1.3 68.2 + - + +
713A ILE* 3.3 8.4 + - + +
714A PHE* 2.9 44.3 + + + -
750A ILE* 4.4 14.8 - - + -
754A HIS* 3.7 39.0 - + + -
757A ILE* 4.4 8.5 - - + -
758A ILE* 3.9 18.8 - - + -
761A TYR* 3.7 31.0 - + + -
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Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A LYS* 2.8 30.9 + - + +
708A ASN* 3.2 19.3 - - - +
710A PHE* 1.3 77.6 - - + +
712A VAL* 1.3 62.6 + - + +
714A PHE* 3.9 2.3 - - + +
715A GLN* 3.0 43.8 + - - +
761A TYR* 5.1 8.5 - - + -
764A THR* 4.0 30.3 - - + -
765A LEU* 5.8 2.9 - - + -
769A LEU* 4.1 21.0 - - + +
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Residues in contact with VAL 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A ALA* 5.0 5.6 - - + +
620A ALA* 3.8 25.4 - - + -
621A ASN* 4.3 17.5 - - - +
708A ASN* 2.7 42.3 + - - +
709A LEU* 3.0 7.6 + - - +
711A LEU* 1.3 69.9 - - + +
713A ILE* 1.3 57.0 + - - +
714A PHE 2.6 16.0 + - - -
715A GLN* 3.0 11.9 + - - +
716A ARG* 2.9 39.5 + - + +
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Residues in contact with ILE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A ALA* 4.8 5.4 - - + -
624A PHE* 3.9 19.4 - - + -
641A LEU* 4.3 17.5 - - + -
645A ILE* 3.9 23.1 - - + -
709A LEU* 2.8 50.6 + - + +
710A PHE* 3.3 15.9 + - + +
712A VAL* 1.3 73.3 - - - +
714A PHE* 1.3 59.3 + - + +
716A ARG* 4.7 1.1 - - - -
717A PHE* 2.9 53.3 + - + +
750A ILE* 4.6 15.7 - - + -
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Residues in contact with PHE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A PHE* 2.9 39.7 + + + +
711A LEU* 4.7 1.1 - - + -
712A VAL 2.6 5.3 + - - -
713A ILE* 1.3 75.6 - - + +
715A GLN* 1.3 58.3 + - - +
716A ARG 3.0 1.3 - - - -
717A PHE* 2.5 26.3 + + - +
718A ILE* 2.7 17.9 + - + +
747A LEU* 3.6 24.2 - - + -
750A ILE* 4.3 23.1 - - + -
751A PHE* 3.4 37.5 - + - -
758A ILE* 4.1 16.2 - - + -
761A TYR* 5.9 0.9 - + - -
765A LEU* 3.8 25.8 - - + -
769A LEU* 3.9 16.8 - - + -
770A PHE* 4.2 12.8 - + + -
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Residues in contact with GLN 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711A LEU* 3.0 33.9 + - - +
712A VAL* 3.0 11.0 + - - +
714A PHE* 1.3 78.8 - - - +
716A ARG* 1.3 66.1 + - + +
718A ILE* 3.3 10.6 + - - +
719A MET* 3.1 20.5 + - - +
769A LEU* 3.5 28.4 - - + +
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Residues in contact with ARG 716 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ASN* 2.9 42.7 + - - +
624A PHE* 3.0 64.2 + - + +
625A SER* 4.4 2.2 - - - +
712A VAL* 2.9 32.1 + - + +
713A ILE 4.5 0.4 - - - +
715A GLN* 1.3 79.1 - - + +
717A PHE* 1.3 63.0 + - - +
719A MET* 3.2 33.4 + - - +
720A ILE* 3.2 30.3 + - - +
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Residues in contact with PHE 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A PHE* 3.4 21.5 - + - -
638A TRP* 3.5 33.9 - + - -
713A ILE* 2.9 28.4 + - + +
714A PHE* 2.5 17.1 + + - +
716A ARG* 1.3 71.9 - - - +
718A ILE* 1.3 63.0 + - + -
720A ILE* 3.3 13.9 - - + +
721A LEU* 3.0 28.9 - - + +
743A CYS* 3.3 32.5 - - - -
746A ARG* 3.8 2.0 - - + -
747A LEU* 3.5 50.0 - - + -
750A ILE* 4.0 13.5 - - + -
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Residues in contact with ILE 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A PHE 2.7 23.7 + - - +
715A GLN* 3.8 9.9 - - - +
717A PHE* 1.3 75.8 - - + +
719A MET* 1.3 58.2 + - - +
721A LEU* 3.1 7.0 + - + -
722A THR* 2.9 48.3 + - - +
747A LEU* 5.8 1.6 - - + -
769A LEU* 3.1 35.7 - - + +
770A PHE* 4.2 20.2 - - + -
774A LEU* 3.8 24.7 - - + -
778A ILE* 4.3 12.8 - - + -
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Residues in contact with MET 719 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A GLN 3.1 14.8 + - - +
716A ARG* 3.3 40.4 - - - +
717A PHE 3.2 0.2 - - - -
718A ILE* 1.3 79.1 - - - +
720A ILE* 1.3 59.8 + - + +
721A LEU 3.5 0.2 + - - -
722A THR* 4.8 2.0 - - - -
723A GLU* 3.1 32.9 + - - +
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Residues in contact with ILE 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A PHE* 3.7 23.1 - - + +
632A PHE* 3.5 29.6 - - + -
716A ARG* 3.2 21.8 - - - +
717A PHE* 3.3 11.4 - - + +
719A MET* 1.3 78.9 - - + +
721A LEU* 1.3 59.5 + - - +
723A GLU* 4.0 18.4 - - - +
724A HIS* 4.0 5.5 + - - +
739A TRP* 3.3 30.5 - - + -
743A CYS* 3.4 28.3 - - - -
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A PHE* 3.0 28.9 - - + +
718A ILE* 3.1 5.1 + - - +
720A ILE* 1.3 77.4 - - - +
722A THR* 1.3 56.7 + - - +
723A GLU 2.8 3.4 - - - -
724A HIS* 2.5 28.4 + - - +
725A LEU* 2.8 16.0 + - + +
739A TRP* 5.4 1.3 - - + -
740A TYR* 4.3 17.0 - - + -
743A CYS* 3.5 28.0 - - + -
744A ILE* 4.0 23.6 - - + +
747A LEU* 3.5 32.5 - - + -
778A ILE* 3.8 23.3 - - + -
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Residues in contact with THR 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A ILE* 2.9 34.7 + - - +
719A MET* 4.8 2.7 - - - -
721A LEU* 1.3 74.0 - - - +
723A GLU* 1.3 60.5 + - - +
725A LEU* 4.2 7.6 - - + -
726A VAL* 3.1 38.9 + - + +
774A LEU* 6.3 0.9 - - - -
775A ASP* 5.0 13.7 - - + +
778A ILE* 3.6 11.3 - - + +
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Residues in contact with GLU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A MET* 3.1 30.5 + - - +
720A ILE* 4.0 17.6 - - - +
721A LEU 2.7 0.6 + - - -
722A THR* 1.3 81.3 - - - +
724A HIS* 1.3 56.5 + - - +
726A VAL* 4.6 2.1 - - - +
727A ARG* 3.4 40.9 + - - +
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Residues in contact with HIS 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ILE 4.0 11.4 - - - +
721A LEU* 2.5 14.8 + - - +
723A GLU* 1.3 75.6 - - - +
725A LEU* 1.3 64.6 + - - +
726A VAL 3.3 0.2 - - - -
727A ARG* 3.3 30.6 + - - +
728A CYS* 3.1 38.2 + - - +
735A VAL* 3.3 28.1 + - + -
737A THR* 3.3 29.1 + - + -
739A TRP* 4.1 21.2 - + + -
740A TYR* 3.8 24.2 - + + -
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 2.8 16.2 + - + +
722A THR* 4.0 5.6 - - + +
724A HIS* 1.3 80.4 - - + +
726A VAL* 1.3 62.4 + - + +
728A CYS* 3.8 3.6 + - - +
729A GLU* 3.3 20.6 + - - +
735A VAL* 3.8 31.4 - - + +
740A TYR* 4.2 12.3 - - + +
775A ASP* 3.5 41.7 - - + +
777A HIS* 3.9 25.6 - - + +
778A ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A THR* 3.1 31.1 + - + +
723A GLU* 4.8 2.2 - - - +
725A LEU* 1.3 76.4 - - + +
727A ARG* 1.3 58.7 + - - +
729A GLU* 3.5 9.9 - - + +
730A THR* 2.9 42.6 + - - +
775A ASP* 5.9 1.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il